Publications 2019

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152 publications

PubMed DOI Crossref
A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.
Uhlen M, Karlsson MJ, Zhong W, ..., Fagerberg L, Brodin P
Science (New York, N.Y.) 366 (6472) eaax9198 [2019-12-20; online 2019-12-21]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
High genetic diversity but no geographical structure of Aedes albopictus populations in Réunion Island.
Latreille AC, Milesi P, Magalon H, Mavingui P, Atyame CM
Parasit Vectors 12 (1) 597 [2019-12-19; online 2019-12-19]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
MPRAscore: robust and non-parametric analysis of massively parallel reporter assays.
Niroula A, Ajore R, Nilsson B
Bioinformatics 35 (24) 5351-5353 [2019-12-15; online 2019-07-31]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
Magda Bienko SciLifeLab Fellow
PubMed DOI Crossref
InfleCS: Clustering Free Energy Landscapes with Gaussian Mixtures.
Westerlund AM, Delemotte L
J Chem Theory Comput 15 (12) 6752-6759 [2019-12-10; online 2019-11-07]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Overeating Saturated Fat Promotes Fatty Liver and Ceramides Compared With Polyunsaturated Fat: A Randomized Trial.
Rosqvist F, Kullberg J, Ståhlman M, ..., Ahlström H, Risérus U
J. Clin. Endocrinol. Metab. 104 (12) 6207-6219 [2019-12-01; online 2019-08-02]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Nascent RNA analyses: tracking transcription and its regulation.
Wissink EM, Vihervaara A, Tippens ND, Lis JT
Nat. Rev. Genet. 20 (12) 705-723 [2019-12-00; online 2019-08-09]
Anniina Vihervaara SciLifeLab Fellow
DOI Crossref
Fluorescence microscopy at the molecular scale
Alvelid J, Testa I
Current Opinion in Biomedical Engineering 12 (-) 34-42 [2019-12-00; online 2019-12-00]
Ilaria Testa SciLifeLab Fellow
PubMed DOI Crossref
Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer.
Gaiser RA, Halimi A, Alkharaan H, ..., Del Chiaro M, Sällberg Chen M
Gut 68 (12) 2186-2194 [2019-12-00; online 2019-03-14]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.
Wei W, Hennig BP, Wang J, ..., Steinmetz LM, Pelechano V
Genome Res 29 (12) 1974-1984 [2019-12-00; online 2019-11-18]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
Cardiac expression of the microsomal triglyceride transport protein protects the heart function during ischemia.
Klevstig M, Arif M, Mannila M, ..., Ehrenborg E, Borén J
J. Mol. Cell. Cardiol. 137 (-) 1-8 [2019-12-00; online 2019-09-15]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees.
Milesi P, Berlin M, Chen J, ..., Karlsson B, Lascoux M
Evol Appl 12 (10) 1946-1959 [2019-12-00; online 2019-08-22]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Helix breaking transition in the S4 of HCN channel is critical for hyperpolarization-dependent gating.
Kasimova MA, Tewari D, Cowgill JB, ..., Delemotte L, Chanda B
Elife 8 (-) - [2019-11-27; online 2019-11-27]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
The human secretome.
Uhlén M, Karlsson MJ, Hober A, ..., Fagerberg L, Sivertsson Å
Sci Signal 12 (609) eaaz0274 [2019-11-26; online 2019-11-26]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations.
Benson E, Lolaico M, Tarasov Y, Gådin A, Högberg B
ACS Nano 13 (11) 12591-12598 [2019-11-26; online 2019-10-15]
Erik Benson SciLifeLab Fellow
PubMed DOI Crossref
Effects of sampling strategy and DNA extraction on human skin microbiome investigations.
Bjerre RD, Hugerth LW, Boulund F, ..., Johansen JD, Engstrand L
Sci Rep 9 (1) 17287 [2019-11-21; online 2019-11-21]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Metabolically Active Brown Adipose Tissue Is Found in Adult Subjects with Type 1 Diabetes.
Eriksson O, Selvaraju RK, Berglund M, Espes D
Int J Mol Sci 20 (23) 5827 [2019-11-20; online 2019-11-20]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Structure of a mitochondrial ATP synthase with bound native cardiolipin.
Mühleip A, McComas SE, Amunts A
Elife 8 (-) - [2019-11-18; online 2019-11-18]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
More Favorable Palmitic Acid Over Palmitoleic Acid Modification of Wnt3 Ensures Its Localization and Activity in Plasma Membrane Domains.
Azbazdar Y, Ozalp O, Sezgin E, ..., Karaca E, Ozhan G
Front Cell Dev Biol 7 (-) 281 [2019-11-15; online 2019-11-15]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
ProTstab - predictor for cellular protein stability.
Yang Y, Ding X, Zhu G, ..., Lv Q, Vihinen M
BMC Genomics 20 (1) 804 [2019-11-04; online 2019-11-04]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Systems biology perspective for studying the gut microbiota in human physiology and liver diseases.
Altay O, Nielsen J, Uhlen M, Boren J, Mardinoglu A
EBioMedicine 49 (-) 364-373 [2019-11-00; online 2019-10-18]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Molecular imaging mass spectrometry for probing protein dynamics in neurodegenerative disease pathology.
Michno W, Wehrli PM, Blennow K, Zetterberg H, Hanrieder J
J. Neurochem. 151 (4) 488-506 [2019-11-00; online 2018-11-06]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.
Barandun J, Hunziker M, Vossbrinck CR, Klinge S
Nat. Microbiol 4 (11) 1798-1804 [2019-11-00; online 2019-07-22]
Jonas Barandun SciLifeLab Fellow
PubMed DOI Crossref
Chemometric Strategies for Sensitive Annotation and Validation of Anatomical Regions of Interest in Complex Imaging Mass Spectrometry Data.
Wehrli PM, Michno W, Blennow K, Zetterberg H, Hanrieder J
J. Am. Soc. Mass Spectrom. 30 (11) 2278-2288 [2019-11-00; online 2019-09-16]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Association of PTHrP levels in CSF with Alzheimer's disease biomarkers.
Kushnir MM, Michno W, Rockwood AL, ..., Strathmann FG, Hanrieder J
Clin Mass Spectrom 14 Pt B (-) 124-129 [2019-11-00; online 2018-10-09]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Sharing Data from Molecular Simulations.
Abraham M, Apostolov R, Barnoud J, ..., Woods C, Zhmurov A
J Chem Inf Model 59 (10) 4093-4099 [2019-10-28; online 2019-10-11]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
The importance of study design in the application of artificial intelligence methods in medicine.
Eklund M, Kartasalo K, Olsson H, Ström P
NPJ Digit Med 2 (-) 101 [2019-10-18; online 2019-10-18]
Kimmo Kartasalo
PubMed DOI Crossref
CUTseq is a versatile method for preparing multiplexed DNA sequencing libraries from low-input samples.
Zhang X, Garnerone S, Simonetti M, ..., Bienko M, Crosetto N
Nat Commun 10 (1) 4732 [2019-10-18; online 2019-10-18]
Magda Bienko SciLifeLab Fellow
PubMed DOI Crossref
Assessment of glucagon receptor occupancy by Positron Emission Tomography in non-human primates.
Eriksson O, Velikyan I, Haack T, ..., Pierrou S, Wagner M
Sci Rep 9 (1) 14960 [2019-10-18; online 2019-10-18]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Dual Bioorthogonal Labeling of the Amyloid-β Protein Precursor Facilitates Simultaneous Visualization of the Protein and Its Cleavage Products.
van Husen LS, Schedin-Weiss S, Trung MN, ..., Elsässer SJ, Tjernberg LO
J. Alzheimers Dis. 72 (2) 537-548 [2019-10-15; online 2019-10-15]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Characterization of transgenic mouse models targeting neuromodulatory systems reveals organizational principles of the dorsal raphe.
Cardozo Pinto DF, Yang H, Pollak Dorocic I, ..., Smidt MP, Lammel S
Nat Commun 10 (1) 4633 [2019-10-11; online 2019-10-11]
Iskra Pollak Dorocic SciLifeLab Fellow
PubMed DOI Crossref
Remodeling the genome with DNA twists.
Bowman GD, Deindl S
Science (New York, N.Y.) 366 (6461) 35-36 [2019-10-04; online 2019-10-12]
SciLifeLab Fellow Sebastian Deindl
PubMed DOI Crossref
Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.
Bengtsson-Palme J, Milakovic M, Švecová H, ..., Grabic R, Udikovic-Kolic N
Water Res 162 (-) 437-445 [2019-10-01; online 2019-07-04]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
VGLUT2 rs2290045 genotype moderates environmental sensitivity to alcohol-related problems in three samples of youths.
Vrettou M, Nilsson KW, Tuvblad C, ..., Nylander I, Comasco E
Eur Child Adolesc Psychiatry 28 (10) 1329-1340 [2019-10-00; online 2019-02-25]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Pancreatic perfusion and its response to glucose as measured by simultaneous PET/MRI.
Espes D, Manell E, Rydén A, ..., Jansson L, Eriksson O
Acta diabetologica 56 (10) 1113-1120 [2019-10-00; online 2019-04-26]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
High-definition spatial transcriptomics for in situ tissue profiling.
Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL
Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]
Sanja Vickovic SciLifeLab Fellow
PubMed DOI Crossref
Genetic basis and timing of a major mating system shift in Capsella.
Bachmann JA, Tedder A, Laenen B, ..., Castric V, Slotte T
New Phytol. 224 (1) 505-517 [2019-10-00; online 2019-08-01]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Association between Transcription Factor AP-2B genotype, obesity, insulin resistance and dietary intake in a longitudinal birth cohort study.
Joost U, Villa I, Comasco E, ..., Veidebaum T, Harro J
Int J Obes (Lond) 43 (10) 2095-2106 [2019-10-00; online 2019-06-17]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
EvoChromo: towards a synthesis of chromatin biology and evolution.
Drinnenberg IA, Berger F, Elsässer SJ, ..., Warnecke T, Wolfe KH
Development 146 (19) - [2019-09-26; online 2019-09-26]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.
Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C
Elife 8 (-) - [2019-09-25; online 2019-09-25]
Marc Friedländer SciLifeLab Fellow
PubMed DOI Crossref
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.
Ray J, Munn PR, Vihervaara A, ..., Danko CG, Lis JT
Proc. Natl. Acad. Sci. U.S.A. 116 (39) 19431-19439 [2019-09-24; online 2019-09-10]
Anniina Vihervaara SciLifeLab Fellow
PubMed DOI Crossref
What industry can teach academia.
Mao Y
Science (New York, N.Y.) 365 (6459) 1342 [2019-09-20; online 2019-10-12]
SciLifeLab Fellow Yumeng Mao
PubMed DOI Crossref
Quantitative Multiplexed ChIP Reveals Global Alterations that Shape Promoter Bivalency in Ground State Embryonic Stem Cells.
Kumar B, Elsässer SJ
Cell Reports 28 (12) 3274-3284.e5 [2019-09-17; online 2019-09-19]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Mechanical properties of plasma membrane vesicles correlate with lipid order, viscosity and cell density.
Steinkühler J, Sezgin E, Urbančič I, Eggeling C, Dimova R
Commun Biol 2 (-) 337 [2019-09-13; online 2019-09-13]
Erdinc Sezgin SciLifeLab Fellow
DOI Crossref
Strategies to Reduce or Eliminate Resistant Pathogens in the Environment
Bengtsson‐Palme J, Heß S
Antibiotic Drug Resistance - (-) 637-673 [2019-09-09; online 2019-08-23]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data
Magesh S, Jonsson V, Bengtsson-Palme J
MBMG 3 (-) - [2019-09-04; online 2019-09-04]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Insights Into Enhanced Complement Activation by Structures of Properdin and Its Complex With the C-Terminal Domain of C3b.
van den Bos RM, Pearce NM, Granneman J, Brondijk THC, Gros P
Front Immunol 10 (-) 2097 [2019-09-04; online 2019-09-04]
DDLS Fellow Nicholas Pearce
PubMed DOI Crossref
Streptococcal sagA activates a proinflammatory response in mast cells by a sublytic mechanism.
von Beek C, Waern I, Eriksson J, ..., Guss B, Pejler G
Cell. Microbiol. 21 (9) e13064 [2019-09-00; online 2019-07-07]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut.
Bakkeren E, Huisman JS, Fattinger SA, ..., Diard M, Hardt WD
Nature 573 (7773) 276-280 [2019-09-00; online 2019-09-04]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Investigation of the skin microbiome: swabs vs. biopsies.
Prast-Nielsen S, Tobin AM, Adamzik K, ..., Engstrand L, Fry L
Br. J. Dermatol. 181 (3) 572-579 [2019-09-00; online 2019-05-06]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Impact of demography on linked selection in two outcrossing Brassicaceae species.
Mattila TM, Laenen B, Horvath R, ..., Savolainen O, Slotte T
Ecol Evol 9 (17) 9532-9545 [2019-09-00; online 2019-08-13]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce.
Chen J, Li L, Milesi P, ..., Vendramin GG, Lascoux M
Evol Appl 12 (8) 1539-1551 [2019-09-00; online 2019-04-30]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Early life stress and voluntary alcohol consumption in relation to Maoa methylation in male rats.
Bendre M, Granholm L, Drennan R, ..., Nylander I, Comasco E
Alcohol 79 (-) 7-16 [2019-09-00; online 2018-11-08]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Turning Up the Heat: Local Temperature Control During in vivo Imaging of Immune Cells.
Ahl D, Eriksson O, Sedin J, ..., Christoffersson G, Phillipson M
Front Immunol 10 (-) 2036 [2019-08-27; online 2019-08-27]
Gustaf Christoffersson SciLifeLab Fellow
PubMed DOI Crossref
Nanoscale dynamics of cholesterol in the cell membrane.
Pinkwart K, Schneider F, Lukoseviciute M, ..., Eggeling C, Sezgin E
J. Biol. Chem. 294 (34) 12599-12609 [2019-08-23; online 2019-07-03]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Molecular Basis and Ecological Relevance of Caulobacter Cell Filamentation in Freshwater Habitats.
Heinrich K, Leslie DJ, Morlock M, Bertilsson S, Jonas K
MBio 10 (4) - [2019-08-20; online 2019-08-20]
Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
Progress towards the Tree of Eukaryotes.
Keeling PJ, Burki F
Curr. Biol. 29 (16) R808-R817 [2019-08-19; online 2019-08-21]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
MRPS25 mutations impair mitochondrial translation and cause encephalomyopathy.
Bugiardini E, Mitchell AL, Rosa ID, ..., Pitceathly RDS, Spinazzola A
Hum. Mol. Genet. 28 (16) 2711-2719 [2019-08-15; online 2019-05-01]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
LIPG-promoted lipid storage mediates adaptation to oxidative stress in breast cancer.
Cadenas C, Vosbeck S, Edlund K, ..., Marchan R, Hengstler JG
Int. J. Cancer 145 (4) 901-915 [2019-08-15; online 2019-02-07]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Chemoselective probe for detailed analysis of ketones and aldehydes produced by gut microbiota in human samples.
Conway LP, Garg N, Lin W, ..., Löhr JM, Globisch D
Chem. Commun. (Camb.) 55 (62) 9080-9083 [2019-08-11; online 2019-07-09]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.
Rangavittal S, Stopa N, Tomaszkiewicz M, ..., Makova KD, Medvedev P
BMC Genomics 20 (1) 641 [2019-08-09; online 2019-08-09]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5' structure element.
Romilly C, Deindl S, Wagner EGH
Proc. Natl. Acad. Sci. U.S.A. 116 (32) 15901-15906 [2019-08-06; online 2019-07-18]
SciLifeLab Fellow Sebastian Deindl
PubMed DOI Crossref
Tools for Bioimaging Pancreatic β Cells in Diabetes.
Kang NY, Soetedjo AAP, Amirruddin NS, ..., Eriksson O, Teo AKK
Trends in molecular medicine 25 (8) 708-722 [2019-08-00; online 2019-06-06]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Strategies for increasing the throughput of super-resolution microscopies.
Mahecic D, Testa I, Griffié J, Manley S
Curr Opin Chem Biol 51 (-) 84-91 [2019-08-00; online 2019-06-15]
Ilaria Testa SciLifeLab Fellow
PubMed DOI Crossref
Single-cell expression noise and gene-body methylation in Arabidopsis thaliana.
Horvath R, Laenen B, Takuno S, Slotte T
Heredity (Edinb) 123 (2) 81-91 [2019-08-00; online 2019-01-16]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Hypothalamic-pituitary-adrenal axis responsiveness, startle response, and sensorimotor gating in late pregnancy.
Breedh J, Comasco E, Hellgren C, ..., Skalkidou A, Poromaa IS
Psychoneuroendocrinology 106 (-) 1-8 [2019-08-00; online 2019-03-15]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Human prenatal exposure to polychlorinated biphenyls (PCBs) and risk behaviors in adolescence.
Dickerson AS, Ransome Y, Karlsson O
Environ Int 129 (-) 247-255 [2019-08-00; online 2019-05-27]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Elucidating the Reprograming of Colorectal Cancer Metabolism Using Genome-Scale Metabolic Modeling.
Zhang C, Aldrees M, Arif M, ..., Mardinoglu A, Aziz MA
Front Oncol 9 (-) 681 [2019-07-30; online 2019-07-30]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Amyloid fibril polymorphism and cell-specific toxicity in vivo.
Jonson M, Nyström S, Sandberg A, ..., Thor S, Hammarström P
Amyloid 26 (sup1) 136-137 [2019-07-26; online 2019-07-26]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.
Smillie CS, Biton M, Ordovas-Montanes J, ..., Xavier RJ, Regev A
Cell 178 (3) 714-730.e22 [2019-07-25; online 2019-07-28]
Sanja Vickovic SciLifeLab Fellow
PubMed DOI Crossref
Constitutive Serotonin Transporter Reduction Resembles Maternal Separation with Regard to Stress-Related Gene Expression.
Comasco E, Schijven D, de Maeyer H, ..., Sundström-Poromaa I, Olivier JDA
ACS Chem Neurosci 10 (7) 3132-3142 [2019-07-17; online 2019-01-23]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
The Potential Use of Metabolic Cofactors in Treatment of NAFLD.
Mardinoglu A, Ural D, Zeybel M, ..., Uhlén M, Borén J
Nutrients 11 (7) 1578 [2019-07-12; online 2019-07-12]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC.
Nirwan N, Itoh Y, Singh P, ..., Amunts A, Saikrishnan K
Nat Commun 10 (1) 3058 [2019-07-11; online 2019-07-11]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
Coupled Enzymatic Treatment and Mass Spectrometric Analysis for Identification of Glucuronidated Metabolites in Human Samples.
Correia MSP, Rao M, Ballet C, Globisch D
Chembiochem 20 (13) 1678-1683 [2019-07-01; online 2019-05-08]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Regulation of the replication initiator DnaA in Caulobacter crescentus.
Felletti M, Omnus DJ, Jonas K
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1862 (7) 697-705 [2019-07-00; online 2018-01-31]
Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
Plasma Proteomics Analysis Reveals Dysregulation of Complement Proteins and Inflammation in Acquired Obesity-A Study on Rare BMI-Discordant Monozygotic Twin Pairs.
Sahebekhtiari N, Saraswat M, Joenväärä S, ..., Renkonen R, Pietiläinen KH
Proteomics Clin Appl 13 (4) e1800173 [2019-07-00; online 2019-02-05]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Outlining the proton-conduction pathway in otopetrin channels.
Delemotte L
Nat. Struct. Mol. Biol. 26 (7) 528-530 [2019-07-00; online 2019-06-27]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain.
Bigalke JM, Aibara S, Roth R, ..., Amunts A, Sandmark J
Sci Adv 5 (7) eaau4202 [2019-07-00; online 2019-07-31]
Alexey Amunts SciLifeLab Fellow
PubMed DOI Crossref
3D-Printed Whole Prostate Models with Tumor Hotspots Using Dual-Extruder Printer.
Liimatainen K, Latonen L, Kartasalo K, Ruusuvuori P
Annu Int Conf IEEE Eng Med Biol Soc 2019 (-) 2867-2871 [2019-07-00; online 2020-01-18]
Kimmo Kartasalo
PubMed DOI Crossref
The Next Generation of Pattern Recognition Receptor Agonists: Improving Response Rates in Cancer Immunotherapy.
O' Donovan DH, Mao Y, Mele DA
Current medicinal chemistry 27 (34) 5654-5674 [2019-06-30; online 2019-06-30]
SciLifeLab Fellow Yumeng Mao
PubMed DOI Crossref
GPR44 as a Target for Imaging Pancreatic Beta-Cell Mass.
Eriksson O
Current diabetes reports 19 (8) 49 [2019-06-27; online 2019-06-27]
Olof Eriksson SciLifeLab Fellow
DOI Crossref
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B
Front. Ecol. Evol. 7 (-) - [2019-06-20; online 2019-06-20]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Mitotically heritable effects of BMAA on striatal neural stem cell proliferation and differentiation.
Pierozan P, Karlsson O
Cell Death Dis 10 (7) 478 [2019-06-17; online 2019-06-17]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Conformational switches control early maturation of the eukaryotic small ribosomal subunit.
Hunziker M, Barandun J, Buzovetsky O, ..., Molina H, Klinge S
Elife 8 (-) - [2019-06-17; online 2019-06-17]
Jonas Barandun SciLifeLab Fellow
PubMed DOI Crossref
Colitis-induced colorectal cancer and intestinal epithelial estrogen receptor beta impact gut microbiota diversity.
Ibrahim A, Hugerth LW, Hases L, ..., Engstrand L, Williams C
Int. J. Cancer 144 (12) 3086-3098 [2019-06-15; online 2019-01-11]
DDLS Fellow Luisa Hugerth
DOI Crossref
RMetD2: a tool for integration of relative transcriptomics data into Genome-scale metabolic models
Zhang C, Lee S, Bidkhori G, ..., Nielsen J, Mardinoglu A
- - (-) - [2019-06-06; online 2019-06-06]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Regulatory Immune Mechanisms beyond Regulatory T Cells.
Christoffersson G, von Herrath M
Trends Immunol. 40 (6) 482-491 [2019-06-00; online 2019-05-14]
Gustaf Christoffersson SciLifeLab Fellow
PubMed DOI Crossref
Growth-driven displacement of protein aggregates along the cell length ensures partitioning to both daughter cells in Caulobacter crescentus.
Schramm FD, Schroeder K, Alvelid J, Testa I, Jonas K
Mol. Microbiol. 111 (6) 1430-1448 [2019-06-00; online 2019-04-03]
Ilaria Testa Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
Biorelevant intrinsic dissolution profiling in early drug development: Fundamental, methodological, and industrial aspects.
Bergström CAS, Box K, Holm R, ..., Schäfer KJ, Teleki A
Eur J Pharm Biopharm 139 (-) 101-114 [2019-06-00; online 2019-03-09]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Sex differences in IL-17 contribute to chronicity in male versus female urinary tract infection.
Zychlinsky Scharff A, Rousseau M, Lacerda Mariano L, ..., Duffy D, Ingersoll MA
JCI Insight 5 (13) - [2019-05-30; online 2019-05-30]
Camila Consiglio DDLS Fellow
PubMed DOI Crossref
Mucus Architecture and Near-Surface Swimming Affect Distinct Salmonella Typhimurium Infection Patterns along the Murine Intestinal Tract.
Furter M, Sellin ME, Hansson GC, Hardt WD
Cell Reports 27 (9) 2665-2678.e3 [2019-05-28; online 2019-05-30]
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Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms.
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MBio 10 (3) - [2019-05-21; online 2019-05-21]
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Paivandy A, Eriksson J, Melo FR, Sellin ME, Pejler G
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Mikael Sellin SciLifeLab Fellow
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Domingo-Prim J, Endara-Coll M, Bonath F, ..., Huertas P, Visa N
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Davanian H, Gaiser RA, Silfverberg M, ..., Engstrand L, Sällberg Chen M
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Turanli B, Karagoz K, Bidkhori G, ..., Mardinoglu A, Arga KY
Front Genet 10 (-) 420 [2019-05-07; online 2019-05-07]
Adil Mardinoglu SciLifeLab Fellow
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Li D, Kular L, Vij M, ..., Jagodic M, Landén NX
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Magda Bienko SciLifeLab Fellow
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Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition.
Liao Q, Lüking M, Krüger DM, ..., Kasson PM, Lynn Kamerlin SC
J Phys Chem B 123 (17) 3576-3590 [2019-05-02; online 2019-04-18]
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Kryvokhyzha D, Milesi P, Duan T, ..., Glémin S, Lascoux M
PLoS Genet 15 (5) e1008131 [2019-05-00; online 2019-05-13]
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Stress-related genetic polymorphisms in association with peripartum depression symptoms and stress hormones: A longitudinal population-based study.
Skalkidou A, Poromaa IS, Iliadis SI, ..., Freyhult E, Comasco E
Psychoneuroendocrinology 103 (-) 296-305 [2019-05-00; online 2019-02-07]
Erika Comasco SciLifeLab Fellow
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GM1 locates to mature amyloid structures implicating a prominent role for glycolipid-protein interactions in Alzheimer pathology.
Michno W, Wehrli PM, Zetterberg H, Blennow K, Hanrieder J
Biochim Biophys Acta Proteins Proteom 1867 (5) 458-467 [2019-05-00; online 2018-09-28]
SciLifeLab Fellow Wojciech Michno
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<scp>CoordinateCleaner</scp> : Standardized cleaning of occurrence records from biological collection databases
Zizka A, Silvestro D, Andermann T, ..., Zizka V, Antonelli A
Methods Ecol Evol 10 (5) 744-751 [2019-05-00; online 2019-02-24]
DDLS Fellow Tobias Andermann
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Pyroglutamation of amyloid-βx-42 (Aβx-42) followed by Aβ1-40 deposition underlies plaque polymorphism in progressing Alzheimer's disease pathology.
Michno W, Nyström S, Wehrli P, ..., Zetterberg H, Hanrieder J
J Biol Chem 294 (17) 6719-6732 [2019-04-26; online 2019-02-27]
SciLifeLab Fellow Wojciech Michno
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Non-Invasive Imaging Methodologies for Assessment of Radiation Damage to Bone Marrow and Kidneys from Peptide Receptor Radionuclide Therapy.
Ahlstedt J, Johansson E, Sydoff M, ..., Gram M, Eriksson O
Neuroendocrinology 110 (1-2) 130-138 [2019-04-19; online 2019-04-19]
Olof Eriksson SciLifeLab Fellow
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Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling.
Sabantsev A, Levendosky RF, Zhuang X, Bowman GD, Deindl S
Nat Commun 10 (1) 1720 [2019-04-12; online 2019-04-12]
SciLifeLab Fellow Sebastian Deindl
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Receptor-Independent Transfer of Low Density Lipoprotein Cargo to Biomembranes.
Axmann M, Sezgin E, Karner A, ..., Stangl H, Plochberger B
Nano Lett. 19 (4) 2562-2567 [2019-04-10; online 2019-03-08]
Erdinc Sezgin SciLifeLab Fellow
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Gelali E, Girelli G, Matsumoto M, ..., Crosetto N, Bienko M
Nat Commun 10 (1) 1636 [2019-04-09; online 2019-04-09]
Magda Bienko SciLifeLab Fellow
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Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
Maniatis S, Äijö T, Vickovic S, ..., Bonneau R, Phatnani H
Science (New York, N.Y.) 364 (6435) 89-93 [2019-04-05; online 2019-04-06]
Sanja Vickovic SciLifeLab Fellow
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System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection.
Garcia-Moreno M, Noerenberg M, Ni S, ..., Mohammed S, Castello A
Mol. Cell 74 (1) 196-211.e11 [2019-04-04; online 2019-02-21]
SciLifeLab Fellow Vicent Pelechano
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Mature Human White Adipocytes Cultured under Membranes Maintain Identity, Function, and Can Transdifferentiate into Brown-like Adipocytes.
Harms MJ, Li Q, Lee S, ..., Spalding KL, Boucher J
Cell Reports 27 (1) 213-225.e5 [2019-04-02; online 2019-04-04]
Adil Mardinoglu SciLifeLab Fellow
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Case Reports of Pre-clinical Replication Studies in Metabolism and Diabetes.
von Herrath M, Pagni PP, Grove K, ..., Karlsen AE, Petersen JS
Cell Metab. 29 (4) 795-802 [2019-04-02; online 2019-03-14]
Gustaf Christoffersson SciLifeLab Fellow
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New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life.
Strassert JFH, Jamy M, Mylnikov AP, Tikhonenkov DV, Burki F
Mol. Biol. Evol. 36 (4) 757-765 [2019-04-01; online 2019-01-23]
Fabien Burki SciLifeLab Fellow
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Synthesis and preclinical evaluation of the CRTH2 antagonist [11C]MK-7246 as a novel PET tracer and potential surrogate marker for pancreatic beta-cell mass.
Eriksson J, Roy T, Sawadjoon S, ..., Eriksson O, Odell LR
Nucl. Med. Biol. 71 (-) 1-10 [2019-04-00; online 2019-04-13]
Olof Eriksson SciLifeLab Fellow
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Measuring nanoscale diffusion dynamics in cellular membranes with super-resolution STED-FCS.
Sezgin E, Schneider F, Galiani S, ..., Lagerholm BC, Eggeling C
Nat Protoc 14 (4) 1054-1083 [2019-04-00; online 2019-03-06]
Erdinc Sezgin SciLifeLab Fellow
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Liver macrophages regulate systemic metabolism through non-inflammatory factors.
Morgantini C, Jager J, Li X, ..., Bajgar A, Aouadi M
Nat Metab 1 (4) 445-459 [2019-04-00; online 2019-03-25]
Claudia Kutter SciLifeLab Fellow
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Discovery of therapeutic agents for prostate cancer using genome-scale metabolic modeling and drug repositioning.
Turanli B, Zhang C, Kim W, ..., Arga KY, Mardinoglu A
EBioMedicine 42 (-) 386-396 [2019-04-00; online 2019-03-21]
Adil Mardinoglu SciLifeLab Fellow
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Deep Learning in Image Cytometry: A Review.
Gupta A, Harrison PJ, Wieslander H, ..., Sintorn IM, Wählby C
Cytometry A 95 (4) 366-380 [2019-04-00; online 2018-12-19]
Kimmo Kartasalo
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A whole-brain atlas of monosynaptic input targeting four different cell types in the medial prefrontal cortex of the mouse.
Ährlund-Richter S, Xuan Y, van Lunteren JA, ..., Meletis K, Carlén M
Nat. Neurosci. 22 (4) 657-668 [2019-04-00; online 2019-03-18]
Iskra Pollak Dorocic SciLifeLab Fellow
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Comprehensive kinetic and substrate specificity analysis of an arylsulfatase from Helix pomatia using mass spectrometry.
Correia MSP, Ballet C, Meistermann H, Conway LP, Globisch D
Bioorg. Med. Chem. 27 (6) 955-962 [2019-03-15; online 2019-01-30]
Daniel Globisch SciLifeLab Fellow
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Expression of PD-L1 and PD-1 in Chemoradiotherapy-Naïve Esophageal and Gastric Adenocarcinoma: Relationship With Mismatch Repair Status and Survival.
Svensson MC, Borg D, Zhang C, ..., Leandersson K, Jirström K
Front Oncol 9 (-) 136 [2019-03-13; online 2019-03-13]
Adil Mardinoglu SciLifeLab Fellow
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Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake.
Rissanen AJ, Peura S, Mpamah PA, ..., Mäki A, Nykänen H
FEMS Microbiol. Lett. 366 (5) - [2019-03-01; online 2019-02-27]
Sari Peura SciLifeLab Fellow
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Pyruvate kinase L/R is a regulator of lipid metabolism and mitochondrial function.
Liu Z, Zhang C, Lee S, ..., Boren J, Mardinoglu A
Metab. Eng. 52 (-) 263-272 [2019-03-00; online 2019-01-04]
Adil Mardinoglu SciLifeLab Fellow
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Plant microRNAs in human sera are likely contaminants.
Fromm B, Kang W, Rovira C, ..., Friedländer MR, Tosar JP
J Nutr Biochem 65 (-) 139-140 [2019-03-00; online 2018-09-05]
Marc Friedländer SciLifeLab Fellow
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Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa.
Monnahan P, Kolář F, Baduel P, ..., Bomblies K, Yant L
Nat Ecol Evol 3 (3) 457-468 [2019-03-00; online 2019-02-25]
SciLifeLab Fellow Tanja Slotte
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Long-term balancing selection drives evolution of immunity genes in Capsella.
Koenig D, Hagmann J, Li R, ..., Wright SI, Weigel D
Elife 8 (-) - [2019-02-26; online 2019-02-26]
SciLifeLab Fellow Tanja Slotte
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Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha).
Fromm B, Tosar JP, Aguilera F, ..., Bachmann L, Hejnol A
Noncoding RNA 5 (1) 19 [2019-02-22; online 2019-02-22]
Marc Friedländer SciLifeLab Fellow
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First-in-class positron emission tomography tracer for the glucagon receptor.
Velikyan I, Haack T, Bossart M, ..., Wagner M, Eriksson O
EJNMMI Res 9 (1) 17 [2019-02-15; online 2019-02-15]
Olof Eriksson SciLifeLab Fellow
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Heterogeneity of Metabolic Defects in Type 2 Diabetes and Its Relation to Reactive Oxygen Species and Alterations in Beta-Cell Mass.
Elksnis A, Martinell M, Eriksson O, Espes D
Front. Physiol. 10 (-) 107 [2019-02-13; online 2019-02-13]
Olof Eriksson SciLifeLab Fellow
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A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection.
Wright SC, Kozielewicz P, Kowalski-Jahn M, ..., Carlsson J, Schulte G
Nat Commun 10 (1) 667 [2019-02-08; online 2019-02-08]
Jens Carlsson SciLifeLab Fellow
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Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation.
Janasch M, Asplund-Samuelsson J, Steuer R, Hudson EP
J. Exp. Bot. 70 (3) 973-983 [2019-02-05; online 2018-10-30]
Paul Hudson SciLifeLab Fellow
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Structural Patching Fosters Divergence of Mitochondrial Ribosomes.
Petrov AS, Wood EC, Bernier CR, ..., Brown A, Amunts A
Mol. Biol. Evol. 36 (2) 207-219 [2019-02-01; online 2018-12-06]
Alexey Amunts SciLifeLab Fellow
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Smart scanning for low-illumination and fast RESOLFT nanoscopy in vivo.
Dreier J, Castello M, Coceano G, ..., Vicidomini G, Testa I
Nat Commun 10 (1) 556 [2019-02-01; online 2019-02-01]
Ilaria Testa SciLifeLab Fellow
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Transcription-driven chromatin repression of Intragenic transcription start sites.
Nielsen M, Ard R, Leng X, ..., Pelechano V, Marquardt S
PLoS Genet 15 (2) e1007969 [2019-02-00; online 2019-02-01]
SciLifeLab Fellow Vicent Pelechano
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How good are pathogenicity predictors in detecting benign variants?
Niroula A, Vihinen M
PLoS Comput Biol 15 (2) e1006481 [2019-02-00; online 2019-02-11]
Abhishek Niroula DDLS Fellow
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Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis.
Benfeitas R, Bidkhori G, Mukhopadhyay B, ..., Kunos G, Mardinoglu A
EBioMedicine 40 (-) 471-487 [2019-02-00; online 2018-12-31]
Adil Mardinoglu SciLifeLab Fellow
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Discovery of KIRREL as a biomarker for prognostic stratification of patients with thin melanoma.
Lundgren S, Fagerström-Vahman H, Zhang C, ..., Nodin B, Jirström K
Biomark Res 7 (1) 1 [2019-01-14; online 2019-01-14]
Adil Mardinoglu SciLifeLab Fellow
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Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia.
Guzman-Otazo J, Gonzales-Siles L, Poma V, ..., Iñiguez V, Sjöling Å
PLoS ONE 14 (1) e0210735 [2019-01-14; online 2019-01-14]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Negative Association Between Allopregnanolone and Cerebral Serotonin Transporter Binding in Healthy Women of Fertile Age.
Sundström Poromaa I, Comasco E, Bäckström T, ..., Jensen P, Frokjaer VG
Front Psychol 9 (-) 2767 [2019-01-11; online 2019-01-11]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
The Circulating Transcriptome as a Source of Biomarkers for Melanoma.
Solé C, Tramonti D, Schramm M, ..., Middleton MR, Lawrie CH
Cancers (Basel) 11 (1) 70 [2019-01-10; online 2019-01-10]
Marc Friedländer SciLifeLab Fellow
PubMed DOI Crossref
Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity.
Garcia SL, Szekely AJ, Bergvall C, Schattenhofer M, Peura S
mSphere 4 (1) - [2019-01-09; online 2019-01-09]
Sarahi Garcia Sari Peura SciLifeLab Fellow
PubMed DOI Crossref
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
Nilsson RH, Larsson KH, Taylor AFS, ..., Kõljalg U, Abarenkov K
Nucleic Acids Res. 47 (D1) D259-D264 [2019-01-08; online 2018-10-30]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Ascetosporea.
Bass D, Ward GM, Burki F
Curr. Biol. 29 (1) R7-R8 [2019-01-07; online 2019-01-09]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium.
Westermann AJ, Venturini E, Sellin ME, ..., Hardt WD, Vogel J
MBio 10 (1) - [2019-01-02; online 2019-01-02]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
A Neural Circuit Mechanism for Encoding Aversive Stimuli in the Mesolimbic Dopamine System.
de Jong JW, Afjei SA, Pollak Dorocic I, ..., Deisseroth K, Lammel S
Neuron 101 (1) 133-151.e7 [2019-01-02; online 2018-11-29]
Iskra Pollak Dorocic SciLifeLab Fellow
PubMed DOI Crossref
Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
Brown P, RELISH Consortium , Zhou Y
Database (Oxford) 2019 (-) - [2019-01-01; online 2019-01-01]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements.
Andermann T, Fernandes AM, Olsson U, ..., Faircloth BC, Antonelli A
Syst. Biol. 68 (1) 32-46 [2019-01-01; online 2018-05-18]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.
Adl SM, Bass D, Lane CE, ..., Zlatogursky V, Zhang Q
J. Eukaryot. Microbiol. 66 (1) 4-119 [2019-01-00; online 2018-09-27]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
Phylogenomics supports the monophyly of the Cercozoa.
Irwin NAT, Tikhonenkov DV, Hehenberger E, ..., Burki F, Keeling PJ
Mol. Phylogenet. Evol. 130 (-) 416-423 [2019-01-00; online 2018-10-11]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
Introducing ribosomal tandem repeat barcoding for fungi.
Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH
Mol Ecol Resour 19 (1) 118-127 [2019-01-00; online 2018-10-24]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Nanostructured Minerals and Vitamins for Food Fortification and Food Supplementation
Knijnenburg JTN, Posavec L, Teleki A
- - (-) 63-98 [2019-00-00; online 2019-00-00]
Alexandra Teleki SciLifeLab Fellow
DOI Crossref
Assessment and Management of Risks Associated With Antibiotic Resistance in the Environment
Bengtsson-Palme J
Management of Emerging Public Health Issues and Risks: Multidisciplinary Approaches to the Changing Environment - (-) 243-263 [2019-00-00; online 2019-00-00]
DDLS Fellow Johan Bengtsson-Palme
SciLifeLab Data Centre
Publications 9.5.1